[2024-01-24 13:25:29,655] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:29,657] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:29,658] [INFO] DQC Reference Directory: /var/lib/cwl/stg6589ba92-741c-4c1e-9f55-202c64095cfe/dqc_reference
[2024-01-24 13:25:30,936] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:30,937] [INFO] Task started: Prodigal
[2024-01-24 13:25:30,938] [INFO] Running command: gunzip -c /var/lib/cwl/stg026dec13-b779-4bf7-b4c6-8b4e8fa92422/GCF_014384985.1_ASM1438498v1_genomic.fna.gz | prodigal -d GCF_014384985.1_ASM1438498v1_genomic.fna/cds.fna -a GCF_014384985.1_ASM1438498v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:38,919] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:38,919] [INFO] Task started: HMMsearch
[2024-01-24 13:25:38,919] [INFO] Running command: hmmsearch --tblout GCF_014384985.1_ASM1438498v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6589ba92-741c-4c1e-9f55-202c64095cfe/dqc_reference/reference_markers.hmm GCF_014384985.1_ASM1438498v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:39,200] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:39,201] [INFO] Found 6/6 markers.
[2024-01-24 13:25:39,235] [INFO] Query marker FASTA was written to GCF_014384985.1_ASM1438498v1_genomic.fna/markers.fasta
[2024-01-24 13:25:39,235] [INFO] Task started: Blastn
[2024-01-24 13:25:39,236] [INFO] Running command: blastn -query GCF_014384985.1_ASM1438498v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6589ba92-741c-4c1e-9f55-202c64095cfe/dqc_reference/reference_markers.fasta -out GCF_014384985.1_ASM1438498v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:39,900] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:39,903] [INFO] Selected 25 target genomes.
[2024-01-24 13:25:39,904] [INFO] Target genome list was writen to GCF_014384985.1_ASM1438498v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:39,924] [INFO] Task started: fastANI
[2024-01-24 13:25:39,925] [INFO] Running command: fastANI --query /var/lib/cwl/stg026dec13-b779-4bf7-b4c6-8b4e8fa92422/GCF_014384985.1_ASM1438498v1_genomic.fna.gz --refList GCF_014384985.1_ASM1438498v1_genomic.fna/target_genomes.txt --output GCF_014384985.1_ASM1438498v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:25:52,852] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:52,853] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6589ba92-741c-4c1e-9f55-202c64095cfe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:25:52,853] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6589ba92-741c-4c1e-9f55-202c64095cfe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:25:52,870] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:25:52,870] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:25:52,870] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Jutongia huaianensis	strain=NSJ-37	GCA_014384985.1	2763668	2763668	type	True	100.0	993	998	95	conclusive
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	80.0278	82	998	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	79.9357	81	998	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	79.1052	65	998	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_000153905.1	40520	40520	type	True	78.9425	67	998	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_000154065.1	88431	88431	type	True	78.8574	62	998	95	below_threshold
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	78.7422	72	998	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	78.6925	64	998	95	below_threshold
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	78.5919	74	998	95	below_threshold
Jutongia hominis	strain=BX3	GCA_014384965.1	2763664	2763664	type	True	78.5701	160	998	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	77.7657	76	998	95	below_threshold
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	77.3549	81	998	95	below_threshold
Eubacterium ramulus	strain=ATCC 29099	GCA_000469345.1	39490	39490	type	True	77.2839	64	998	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	77.1371	64	998	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:25:52,872] [INFO] DFAST Taxonomy check result was written to GCF_014384985.1_ASM1438498v1_genomic.fna/tc_result.tsv
[2024-01-24 13:25:52,873] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:25:52,874] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:25:52,874] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6589ba92-741c-4c1e-9f55-202c64095cfe/dqc_reference/checkm_data
[2024-01-24 13:25:52,876] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:25:52,908] [INFO] Task started: CheckM
[2024-01-24 13:25:52,908] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014384985.1_ASM1438498v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014384985.1_ASM1438498v1_genomic.fna/checkm_input GCF_014384985.1_ASM1438498v1_genomic.fna/checkm_result
[2024-01-24 13:26:21,993] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:21,994] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:22,013] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:22,013] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:22,014] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014384985.1_ASM1438498v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:22,014] [INFO] Task started: Blastn
[2024-01-24 13:26:22,014] [INFO] Running command: blastn -query GCF_014384985.1_ASM1438498v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6589ba92-741c-4c1e-9f55-202c64095cfe/dqc_reference/reference_markers_gtdb.fasta -out GCF_014384985.1_ASM1438498v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:23,121] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:23,126] [INFO] Selected 13 target genomes.
[2024-01-24 13:26:23,126] [INFO] Target genome list was writen to GCF_014384985.1_ASM1438498v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:23,180] [INFO] Task started: fastANI
[2024-01-24 13:26:23,180] [INFO] Running command: fastANI --query /var/lib/cwl/stg026dec13-b779-4bf7-b4c6-8b4e8fa92422/GCF_014384985.1_ASM1438498v1_genomic.fna.gz --refList GCF_014384985.1_ASM1438498v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014384985.1_ASM1438498v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:30,855] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:30,869] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:30,869] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_003481585.1	s__Butyribacter sp001916135	98.669	893	998	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyribacter	95.0	98.94	98.22	0.93	0.89	9	conclusive
GCA_900759665.1	s__Butyribacter sp900759665	89.8066	698	998	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyribacter	95.0	98.02	98.02	0.87	0.87	2	-
GCA_902788645.1	s__Butyribacter sp902788645	87.9769	589	998	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003478445.1	s__Butyribacter sp003524945	82.6306	596	998	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyribacter	95.0	98.75	98.31	0.94	0.90	7	-
GCF_003478335.1	s__Butyribacter sp003529475	80.5435	194	998	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyribacter	95.0	98.38	97.93	0.91	0.89	10	-
GCA_014337155.1	s__CAG-127 sp900319515	78.9084	86	998	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127	95.0	98.02	96.09	0.90	0.85	25	-
GCA_017626435.1	s__Butyribacter sp017626435	77.8657	123	998	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910575435.1	s__Butyribacter sp910575435	76.8241	76	998	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyribacter	95.0	100.00	100.00	0.99	0.99	2	-
GCA_017476305.1	s__Butyribacter sp017476305	76.779	64	998	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Butyribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:30,871] [INFO] GTDB search result was written to GCF_014384985.1_ASM1438498v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:30,872] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:30,875] [INFO] DFAST_QC result json was written to GCF_014384985.1_ASM1438498v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:30,875] [INFO] DFAST_QC completed!
[2024-01-24 13:26:30,875] [INFO] Total running time: 0h1m1s